Marizanne Kapp has been given "compassionate leave" and will miss South Africa's match against India in the final of a triangular women's Twenty20 series in East London on Thursday.
Head coach Hilton Moreeng confirmed Kapp's absence, which followed the omission of her wife and former captain Dane van Niekerk from South Africa's squad for the Women's T20 World Cup which starts in Cape Town on February 10.
But Moreeng said Kapp would play in the World Cup, saying she was part of the squad and "committed to us".
"We granted her leave so she can come to the World Cup and be ready to play," he added, speaking at a pre-match press conference.
Moreeng said Van Niekerk remained in the frame for future selection despite failing to meet Cricket South Africa's fitness requirements ahead of the World Cup.
It has been widely reported that Van Niekerk only failed in one category, missing a target of running two kilometres in nine minutes and 30 seconds by 18 seconds.
Kapp tweeted her support of Van Niekerk after the World Cup squad announcement and on Wednesday morning posted a picture of a swimming pool with the caption, "Patiently waiting for the WPL auction".
Kapp, 33, and Van Niekerk, 29, have had long international careers. They made their international debuts in 2008/09 and are expected to feature in the auction for the Women's Indian Premier League (WPL), likely to take place within the next two weeks.
Both players have already been successful in franchise competitions in Australia and England.
The controversy over Van Niekerk's omission has led to speculation that both players may opt to concentrate on playing franchise cricket in the future.
South Africa are already without Wisden's Women's Cricketer of the Year Lizelle Lee, who retired suddenly last year after also struggling to maintain CSA's fitness standards, and another former captain, Mignon du Preez, who has retired.
Van Niekerk described herself as "absolutely broken" after being left out of South Africa's World Cup squad.